We describe sensitive and quantitative assays for measuring o-tyrosine, m-tyrosine, o,o'-dityrosine, 3-nitrotyrosine and 3-cholorotyrosine in proteins and tissues. The methods combine gas chromatography (GC) with isotope dilution negative-ion electron capture mass spectrometry (MS). GC/MS has enabled us to determine the relative amounts of oxidized amino acids in proteins and lipoproteins oxidized in vitro. We also have used this approach to quantify levels of modified amino acids in atherosclerotic lesions, inflammatory tissues, and tissue proteins of aging animals. Our observations indicate that the quantitative evaluation of protein oxidation products by GC/MS is a powerful tool for identifying pathways that promote oxidative protein modification in vivo.